Hi all, Does anyone know of an existing function in any package to normalize an AffyBatch object using a set of control probesets only? I've looked through the functions in the affy package and searched the archives, but couldn't find anything. There is an option similar to what I want in the normalizeWithinArrays(method="control") function in limma, but I wanted to find out if I had missed something before trying to write my own function. Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

OK, I should have kept looking a little more before I sent out this message. It appears that the normalize.AffyBatch.loess() method can accept a subset of the data. Has anyone used this method successfully? I'm not sure how the subset of probes should be indicated - perhaps by their row numbers from exprs(affybatchobject)? Jenny At 01:56 PM 9/27/2006, Jenny Drnevich wrote: >Hi all, > >Does anyone know of an existing function in any package to normalize an >AffyBatch object using a set of control probesets only? I've looked through >the functions in the affy package and searched the archives, but couldn't >find anything. There is an option similar to what I want in the >normalizeWithinArrays(method="control") function in limma, but I wanted to >find out if I had missed something before trying to write my own function. > >Thanks, >Jenny > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: drnevich at uiuc.edu > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor